Ministers insisted that sums being spent on the privately-sponsored independent state schools - which have attracted accusations of being unnecessarily lavish - are in line with other inner-city comprehensives.
Figures detailing spending on the 23 academies due to open in the next two or three years show that they will cost pound;29.9m each - an average of Pounds 23,370 per pupil. The costs are 50 per cent more than the average pound;16,000 per pupil which is spent building other new secondary schools across the country.
But this week the Department for Education and Skills insisted that comparisons were unfair because building costs in the inner-cities - half of academies are in London - are much more and are therefore not unreasonable.
According to new figures, the most expensive academy so far is the Thomas Deacon academy, in Peterborough, at pound;46.5million, although it replaces three secondary schools.
A funding agreement between ministers and the academy's sponsors, the Deacon's School Trust and Perkins Engines, an engineering firm, show that the school will have 2,200 pupils at a cost of pound;21,105 per pupil.
Of the new academies, the most expensive per pupil will be the Bridge academy in Hackney, east London, sponsored by UBS.
With just 1,150 pupils and a funding pot of pound;34.7m, it will cost an estimated pound;30,164 per pupil, almost twice that of other new secondaries.
The academy, being built on a brownfield site alongside the Grand Union canal, is a futuristic, seven-storey building on split levels and is almost entirely open-plan. It has been dubbed a "school without corridors".
The Petchey academy, also in Hackney, is named as the second-most expensive to build. The academy, sponsored by Jack Petchey, a property entrepreneur, and due to open in September, cost pound;34.2m and has 1,200 places - equal to Pounds 28,512 per pupil.
But a spokesman for the DfES said: "The average cost of a new secondary school in a high cost inner-city area is similar for academy and non-academy schools. "The average cost of a new secondary school with 1,300 pupils and a sixth form in a high-cost inner-city area is pound;25m to pound;30m and some non-academy schools now under construction are costing up to pound;35 million. The average cost of an academy, of this size and location is similarly pound;25m to 30m."
A total of 27 academies have opened so far. The most expensive of these is the Haberdashers' Aske's Knights academy in south London, at pound;38m.
According to the latest figures, published by the DfES in response to a written Parliamentary question from Sarah Teather, the Liberal Democrat education spokeswoman, the next 23 academies will cost just under pound;30m each to build.
After Thomas Deacon academy, the next most expensive is Folkestone academy, in Kent, which is being sponsored by Roger de Haan, the founder of Saga holidays. It will cost pound;36.7m.